A Drug Target Interaction Prediction Based on LINE-RF Learning

2020 ◽  
Vol 15 (7) ◽  
pp. 750-757
Author(s):  
Jihong Wang ◽  
Yue Shi ◽  
Xiaodan Wang ◽  
Huiyou Chang
Keyword(s):  
Network Topology ◽  
Drug Target ◽  
Large Scale ◽  
Representation Learning ◽  
New Drugs ◽  
Combination Method ◽  
Learning Methods ◽  
Network Representation ◽  
On Line ◽  
Clinical Experiments

Background: At present, using computer methods to predict drug-target interactions (DTIs) is a very important step in the discovery of new drugs and drug relocation processes. The potential DTIs identified by machine learning methods can provide guidance in biochemical or clinical experiments. Objective: The goal of this article is to combine the latest network representation learning methods for drug-target prediction research, improve model prediction capabilities, and promote new drug development. Methods: We use large-scale information network embedding (LINE) method to extract network topology features of drugs, targets, diseases, etc., integrate features obtained from heterogeneous networks, construct binary classification samples, and use random forest (RF) method to predict DTIs. Results: The experiments in this paper compare the common classifiers of RF, LR, and SVM, as well as the typical network representation learning methods of LINE, Node2Vec, and DeepWalk. It can be seen that the combined method LINE-RF achieves the best results, reaching an AUC of 0.9349 and an AUPR of 0.9016. Conclusion: The learning method based on LINE network can effectively learn drugs, targets, diseases and other hidden features from the network topology. The combination of features learned through multiple networks can enhance the expression ability. RF is an effective method of supervised learning. Therefore, the Line-RF combination method is a widely applicable method.

scholarly journals DLDTI: A learning-based framework for identification of drug-target interaction using neural networks and network representation

2020 ◽  
Author(s):  
Yihan Zhao ◽  
Kai Zheng ◽  
Baoyi Guan ◽  
Mengmeng Guo ◽  
Lei Song ◽  
...  
Keyword(s):  
Neural Networks ◽  
Drug Target ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Representation Learning ◽  
Heterogeneous Data ◽  
Biological Data ◽  
Mapping Space ◽  
Network Representation ◽  
Low Dimensional

AbstractTo elucidate novel molecular mechanisms of known drugs, efficient and feasible computational methods for predicting potential drug-target interactions (DTI) would be of great importance. A novel calculation model called DLDTI was generated for predicting DTI based on network representation learning and convolutional neural networks. The proposed approach simultaneously fuses the topology of complex networks and diverse information from heterogeneous data sources and copes with the noisy, incomplete, and high-dimensional nature of large-scale biological data by learning low-dimensional and rich depth features of drugs and proteins. Low-dimensional feature vectors were used to train DLDTI to obtain optimal mapping space and infer new DTIs by ranking DTI candidates based on their proximity to optimal mapping space. DLDTI achieves promising performance under 5-fold cross-validation with AUC values of 0.9172, which was higher than that of the method based on different classifiers or different feature combination technique. Moreover, biomedical experiments were also completed to validate DLDTI’s performance. Consistent with the predicted result, tetramethylpyrazine, a member of pyrazines, reduced atherosclerosis progression and inhibited signal transduction in platelets, via PI3K/Akt, cAMP and calcium signaling pathways. The source code and datasets explored in this work are available at https://github.com/CUMTzackGit/DLDTI

scholarly journals A Novel Method to Predict Drug-Target Interactions Based on Large-Scale Graph Representation Learning

Cancers ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 2111
Author(s):  
Bo-Wei Zhao ◽  
Zhu-Hong You ◽  
Lun Hu ◽  
Zhen-Hao Guo ◽  
Lei Wang ◽  
...  
Keyword(s):  
Drug Target ◽  
Large Scale ◽  
Computational Models ◽  
Structural Information ◽  
Characteristic Curve ◽  
Representation Learning ◽  
Graph Representation ◽  
Convolutional Network ◽  
Novel Method

Identification of drug-target interactions (DTIs) is a significant step in the drug discovery or repositioning process. Compared with the time-consuming and labor-intensive in vivo experimental methods, the computational models can provide high-quality DTI candidates in an instant. In this study, we propose a novel method called LGDTI to predict DTIs based on large-scale graph representation learning. LGDTI can capture the local and global structural information of the graph. Specifically, the first-order neighbor information of nodes can be aggregated by the graph convolutional network (GCN); on the other hand, the high-order neighbor information of nodes can be learned by the graph embedding method called DeepWalk. Finally, the two kinds of feature are fed into the random forest classifier to train and predict potential DTIs. The results show that our method obtained area under the receiver operating characteristic curve (AUROC) of 0.9455 and area under the precision-recall curve (AUPR) of 0.9491 under 5-fold cross-validation. Moreover, we compare the presented method with some existing state-of-the-art methods. These results imply that LGDTI can efficiently and robustly capture undiscovered DTIs. Moreover, the proposed model is expected to bring new inspiration and provide novel perspectives to relevant researchers.

scholarly journals Prediction of drug-target interactions from multi-molecular network based on LINE network representation method

2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Bo-Ya Ji ◽  
Zhu-Hong You ◽  
Han-Jing Jiang ◽  
Zhen-Hao Guo ◽  
Kai Zheng
Keyword(s):  
Computational Methods ◽  
Information Integration ◽  
Drug Target ◽  
Large Scale ◽  
New Drugs ◽  
Single Type ◽  
Information Network ◽  
Potential Drug Target ◽  
Potential Drug ◽  
Network Embedding

Abstract Background The prediction of potential drug-target interactions (DTIs) not only provides a better comprehension of biological processes but also is critical for identifying new drugs. However, due to the disadvantages of expensive and high time-consuming traditional experiments, only a small section of interactions between drugs and targets in the database were verified experimentally. Therefore, it is meaningful and important to develop new computational methods with good performance for DTIs prediction. At present, many existing computational methods only utilize the single type of interactions between drugs and proteins without paying attention to the associations and influences with other types of molecules. Methods In this work, we developed a novel network embedding-based heterogeneous information integration model to predict potential drug-target interactions. Firstly, a heterogeneous multi-molecuar information network is built by combining the known associations among protein, drug, lncRNA, disease, and miRNA. Secondly, the Large-scale Information Network Embedding (LINE) model is used to learn behavior information (associations with other nodes) of drugs and proteins in the network. Hence, the known drug-protein interaction pairs can be represented as a combination of attribute information (e.g. protein sequences information and drug molecular fingerprints) and behavior information of themselves. Thirdly, the Random Forest classifier is used for training and prediction. Results In the results, under the five-fold cross validation, our method obtained 85.83% prediction accuracy with 80.47% sensitivity at the AUC of 92.33%. Moreover, in the case studies of three common drugs, the top 10 candidate targets have 8 (Caffeine), 7 (Clozapine) and 6 (Pioglitazone) are respectively verified to be associated with corresponding drugs. Conclusions In short, these results indicate that our method can be a powerful tool for predicting potential drug-target interactions and finding unknown targets for certain drugs or unknown drugs for certain targets.

scholarly journals A learning-based method for drug-target interaction prediction based on feature representation learning and deep neural network

2020 ◽  
Vol 21 (S13) ◽  
Author(s):  
Jiajie Peng ◽  
Jingyi Li ◽  
Xuequn Shang
Keyword(s):  
Neural Network ◽  
Drug Discovery ◽  
Drug Target ◽  
Deep Neural Network ◽  
Computational Prediction ◽  
Representation Learning ◽  
Feature Representation ◽  
New Drugs ◽  
Target Interaction ◽  
Interaction Prediction

Abstract Background Drug-target interaction prediction is of great significance for narrowing down the scope of candidate medications, and thus is a vital step in drug discovery. Because of the particularity of biochemical experiments, the development of new drugs is not only costly, but also time-consuming. Therefore, the computational prediction of drug target interactions has become an essential way in the process of drug discovery, aiming to greatly reducing the experimental cost and time. Results We propose a learning-based method based on feature representation learning and deep neural network named DTI-CNN to predict the drug-target interactions. We first extract the relevant features of drugs and proteins from heterogeneous networks by using the Jaccard similarity coefficient and restart random walk model. Then, we adopt a denoising autoencoder model to reduce the dimension and identify the essential features. Third, based on the features obtained from last step, we constructed a convolutional neural network model to predict the interaction between drugs and proteins. The evaluation results show that the average AUROC score and AUPR score of DTI-CNN were 0.9416 and 0.9499, which obtains better performance than the other three existing state-of-the-art methods. Conclusions All the experimental results show that the performance of DTI-CNN is better than that of the three existing methods and the proposed method is appropriately designed.

scholarly journals Predicting drug-target interactions from drug structure and protein sequence using novel convolutional neural networks

2019 ◽  
Vol 20 (S25) ◽  
Author(s):  
ShanShan Hu ◽  
Chenglin Zhang ◽  
Peng Chen ◽  
Pengying Gu ◽  
Jun Zhang ◽  
...  
Keyword(s):  
Drug Target ◽  
Large Scale ◽  
New Drugs ◽  
Accurate Identification ◽  
Protein Targets ◽  
Benchmark Datasets ◽  
Practical Tool ◽  
Auc Value ◽  
Improved Performance ◽  
Potential Interactions

Abstract Background Accurate identification of potential interactions between drugs and protein targets is a critical step to accelerate drug discovery. Despite many relative experimental researches have been done in the past decades, detecting drug-target interactions (DTIs) remains to be extremely resource-intensive and time-consuming. Therefore, many computational approaches have been developed for predicting drug-target associations on a large scale. Results In this paper, we proposed an deep learning-based method to predict DTIs only using the information of drug structures and protein sequences. The final results showed that our method can achieve good performance with the accuracies up to 92.0%, 90.0%, 92.0% and 90.7% for the target families of enzymes, ion channels, GPCRs and nuclear receptors of our created dataset, respectively. Another dataset derived from DrugBank was used to further assess the generalization of the model, which yielded an accuracy of 0.9015 and an AUC value of 0.9557. Conclusion It was elucidated that our model shows improved performance in comparison with other state-of-the-art computational methods on the common benchmark datasets. Experimental results demonstrated that our model successfully extracted more nuanced yet useful features, and therefore can be used as a practical tool to discover new drugs. Availability http://deeplearner.ahu.edu.cn/web/CnnDTI.htm.

scholarly journals Structural Hierarchy-Enhanced Network Representation Learning

2020 ◽  
Vol 10 (20) ◽  
pp. 7214
Author(s):  
Cheng-Te Li ◽  
Hong-Yu Lin
Keyword(s):  
Network Topology ◽  
Link Prediction ◽  
Main Idea ◽  
Representation Learning ◽  
Coarse Grained ◽  
Community Knowledge ◽  
Structural Hierarchy ◽  
Network Representation ◽  
Node Classification ◽  
Node Embeddings

Network representation learning (NRL) is crucial in generating effective node features for downstream tasks, such as node classification (NC) and link prediction (LP). However, existing NRL methods neither properly identify neighbor nodes that should be pushed together and away in the embedding space, nor model coarse-grained community knowledge hidden behind the network topology. In this paper, we propose a novel NRL framework, Structural Hierarchy Enhancement (SHE), to deal with such two issues. The main idea is to construct a structural hierarchy from the network based on community detection, and to utilize such a hierarchy to perform level-wise NRL. In addition, lower-level node embeddings are passed to higher-level ones so that community knowledge can be aware of in NRL. Experiments conducted on benchmark network datasets show that SHE can significantly boost the performance of NRL in both tasks of NC and LP, compared to other hierarchical NRL methods.

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